nmr-processing 7.4.3 → 8.2.0

package/lib/assignment/getAssignments.js

@@ -10,7 +10,7 @@ const checkIDs_1 = require("./utils/getAssignment/checkIDs");
 const getTargetsAndCorrelations_1 = require("./utils/getAssignment/getTargetsAndCorrelations");
 const getWorkFlow_1 = __importDefault(require("./utils/getAssignment/getWorkFlow"));
 async function getAssignments(input, options = {}) {
-    let { restrictionByCS = {}, justAssign, minScore = 1, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
+    let { restrictionByCS = {}, justAssign, minScore = 0.01, maxSolutions = 10, nbAllowedUnAssigned, timeout = 6000, predictionOptions = {}, predictions = {}, correlation: correlationOptions = {}, } = options;
     const { tolerance = { H: 0.2, C: 1 }, useChemicalShiftScore = false, chemicalShiftRestriction = true, } = restrictionByCS;
     const molecule = input.molecule;
     if (!molecule)

package/lib/assignment/getAssignments.js.map

@@ -1 +1 @@
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+{"version":3,"file":"getAssignments.js","sourceRoot":"","sources":["../../src/assignment/getAssignments.ts"],"names":[],"mappings":";;;;;;AACA,yDAAsE;AAQtE,6EAIgD;AAChD,6DAA0D;AAC1D,+FAA4F;AAC5F,oFAA4D;AA0ErD,KAAK,UAAU,cAAc,CAClC,KAA6B,EAC7B,UAAiC,EAAE;IAEnC,IAAI,EACF,eAAe,GAAG,EAAE,EACpB,UAAU,EACV,QAAQ,GAAG,IAAI,EACf,YAAY,GAAG,EAAE,EACjB,mBAAmB,EACnB,OAAO,GAAG,IAAI,EACd,iBAAiB,GAAG,EAAE,EACtB,WAAW,GAAG,EAAE,EAChB,WAAW,EAAE,kBAAkB,GAAG,EAAE,GACrC,GAAG,OAAO,CAAC;IAEZ,MAAM,EACJ,SAAS,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,EAC5B,qBAAqB,GAAG,KAAK,EAC7B,wBAAwB,GAAG,IAAI,GAChC,GAAG,eAAe,CAAC;IAEpB,MAAM,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;IAEhC,IAAI,CAAC,QAAQ;QAAE,MAAM,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;IAEpE,QAAQ,CAAC,oBAAoB,EAAE,CAAC;IAChC,IAAA,qDAAiC,EAAC,QAAQ,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,IAAA,mBAAQ,EAAC,KAAK,CAAC,OAAO,CAAC,CAAC;IACxC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,IAAA,qDAAyB,EACzD,OAAO,EACP,kBAAkB,CACnB,CAAC;IAEF,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,qBAAW,EAAC,YAAY,EAAE,UAAU,CAAC,CAAC;IAElE,MAAM,SAAS,GAAG,MAAM,IAAA,mCAAgB,EAAC;QACvC,eAAe,EAAE;YACf,SAAS;YACT,qBAAqB;YACrB,wBAAwB;SACzB;QACD,OAAO;QACP,QAAQ;QACR,OAAO;QACP,QAAQ;QACR,YAAY;QACZ,eAAe;QACf,mBAAmB;QACnB,YAAY;QACZ,OAAO;QACP,iBAAiB;QACjB,WAAW;KACZ,CAAC,CAAC;IAEH,OAAO,SAAS,CAAC;AACnB,CAAC;AAzDD,wCAyDC"}

package/lib/assignment/utils/getAssignment/checkIDs.d.ts

@@ -3,4 +3,4 @@ import type { SpectraData } from '../../getAssignments';
 import type { SpectraDataWithIds, NMRRangeWithIds, NMRZoneWithIds } from '../../nmrAssigment';
 export declare function checkIDs(input?: SpectraData[]): SpectraDataWithIds[];
 export declare function hasIDs(data: NMRRange[] | NMRZone[]): asserts data is NMRRangeWithIds[] | NMRZoneWithIds[];
-export declare function addIDs(data: NMRRange[] | NMRZone[]): NMRRangeWithIds[] | NMRZoneWithIds[];
+export declare function addIDs<T extends NMRRange[] | NMRZone[]>(data: T): T & (NMRRangeWithIds[] | NMRZoneWithIds[]);

package/lib/assignment/utils/getAssignment/checkIDs.js.map

@@ -1 +1 @@
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package/lib/databases/getDatabase.d.ts

@@ -1,2 +1,7 @@
 import { DatabaseNMREntry } from './DatabaseNMREntry';
-export declare function getDatabase(url?: string): Promise<DatabaseNMREntry[]>;
+export declare function getDatabase(url?: string, options?: {
+    /**
+     * @default 'tsv'
+     */
+    format?: 'tsv' | 'json';
+}): Promise<DatabaseNMREntry[]>;

package/lib/databases/getDatabase.js

@@ -3,13 +3,23 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.getDatabase = void 0;
 const cross_fetch_1 = require("cross-fetch");
 const resurrectRange_1 = require("../utilities/resurrectRange");
-async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing') {
+async function getDatabase(url = 'https://docs.google.com/spreadsheets/d/1uwyq_L38PMRWCcT4If_EhPbHKyY3q_2tpjV8vr5_zh0/edit?usp=sharing', options = {}) {
+    const { format = 'tsv' } = options;
     if (url.includes('google.com')) {
         url = `https://googledocs.cheminfo.org/spreadsheets/d/${extractGoogleUUID(url)}/export?format=tsv`;
     }
+    let parsed;
     const response = await (0, cross_fetch_1.fetch)(url);
-    const result = await response.text();
-    const parsed = parseData(result);
+    switch (format) {
+        case 'tsv':
+            parsed = parseData(await response.text());
+            break;
+        case 'json':
+            parsed = await response.json();
+            break;
+        default:
+            throw new Error('unknown database format');
+    }
     const results = [];
     for (let line of parsed.data) {
         const result = {

package/lib/databases/getDatabase.js.map

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package/lib/index.d.ts

@@ -1,4 +1,4 @@
-export * from './constants/gyromagneticRatio';
+export * from 'gyromagnetic-ratio';
 export * from './constants/impurities';
 export * from './constants/couplingPatterns';
 export * from './peaks/peaksFilterImpurities';
@@ -27,8 +27,10 @@ export * from './xyz/xyzJResAnalyzer';
 export * from './databases/getDatabase';
 export * from './databases/carbonImpurities';
 export * from './databases/protonImpurities';
+export * from './peaks/solventSuppression';
+export * from './ranges/markSolventSignal';
 export type { NMRSignal1D } from './signals/NMRSignal1D';
-export type { NMRSignal2D, Signal2DAxisData } from './xyz/NMRSignal2D';
+export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
 export type { NMRRange } from './xy/NMRRange';
 export type { NMRZone } from './xyz/NMRZone';
 export type { NMRPeak1D } from './peaks/NMRPeak1D';

package/lib/index.js

@@ -14,7 +14,7 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-__exportStar(require("./constants/gyromagneticRatio"), exports);
+__exportStar(require("gyromagnetic-ratio"), exports);
 __exportStar(require("./constants/impurities"), exports);
 __exportStar(require("./constants/couplingPatterns"), exports);
 __exportStar(require("./peaks/peaksFilterImpurities"), exports);
@@ -43,4 +43,6 @@ __exportStar(require("./xyz/xyzJResAnalyzer"), exports);
 __exportStar(require("./databases/getDatabase"), exports);
 __exportStar(require("./databases/carbonImpurities"), exports);
 __exportStar(require("./databases/protonImpurities"), exports);
+__exportStar(require("./peaks/solventSuppression"), exports);
+__exportStar(require("./ranges/markSolventSignal"), exports);
 //# sourceMappingURL=index.js.map

package/lib/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,qDAAmC;AACnC,yDAAuC;AACvC,+DAA6C;AAE7C,gEAA8C;AAE9C,6DAA2C;AAC3C,6DAA2C;AAC3C,2DAAyC;AACzC,2DAAyC;AACzC,2DAAyC;AACzC,0DAAwC;AACxC,iEAA+C;AAE/C,gEAA8C;AAC9C,iEAA+C;AAC/C,8DAA4C;AAE5C,uDAAqC;AACrC,sDAAoC;AAEpC,4DAA0C;AAC1C,wDAAsC;AACtC,yDAAuC;AAEvC,wDAAsC;AACtC,8DAA4C;AAC5C,2DAAyC;AAEzC,0DAAwC;AACxC,2DAAyC;AAEzC,4DAA0C;AAC1C,wDAAsC;AAEtC,0DAAwC;AACxC,+DAA6C;AAC7C,+DAA6C;AAE7C,6DAA2C;AAC3C,6DAA2C"}

package/lib/peaks/NMRPeak1D.d.ts

@@ -2,6 +2,5 @@ import type { PeakXYWidth } from 'cheminfo-types';
 import type { Shape1D } from 'ml-peak-shape-generator';
 export interface NMRPeak1D extends PeakXYWidth {
     kind?: string;
-    fwhm?: number;
     shape?: Shape1D;
 }

package/lib/peaks/peaksToRanges.d.ts

@@ -1,6 +1,7 @@
 import type { DataXY } from 'cheminfo-types';
 import type { NMRRange } from '../xy/NMRRange';
 import type { NMRPeak1D } from './NMRPeak1D';
+import type { SignalIntern } from './util/jAnalyzer';
 export interface OptionsPeaksToRanges {
     /**
      * Number of hydrogens or some number to normalize the integration data. If it's zero return the absolute integration value
@@ -59,4 +60,19 @@ declare type NMRPeak1DIntern = Omit<NMRPeak1D, 'fwhm' | 'shape'>;
  * This function clustering peaks and calculate the integration value for each range from the peak list returned from extractPeaks function.
  */
 export declare function peaksToRanges(data: DataXY, peakList: NMRPeak1DIntern[], options?: OptionsPeaksToRanges): NMRRange[];
+/**
+ * Extract the signals from the peakList and the given spectrum.
+ * @param {object} data - spectra data
+ * @param {array} peakList - nmr signals
+ * @param {object} [options = {}]
+ * @param {number} [options.integrationSum='100'] - Number of hydrogens or some number to normalize the integration data, If it's zero return the absolute integration value
+ * @param {string} [options.integralType='sum'] - option to chose between approx area with peaks or the sum of the points of given range
+ * @param {number} [options.frequencyCluster=16] - distance limit to clustering the peaks.
+ * range = frequencyCluster / observeFrequency -> Peaks withing this range are considered to belongs to the same signal1D
+ * @param {string} [options.nucleus='1H'] - - Nucleus
+ * @param {String} [options.frequency = 400] - Observed frequency
+ * @return {array} nmr signals
+ * @private
+ */
+export declare function detectSignals(data: DataXY, peakList: NMRPeak1DIntern[], options?: OptionsDetectSignals): SignalIntern[];
 export {};

package/lib/peaks/peaksToRanges.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.peaksToRanges = void 0;
+exports.detectSignals = exports.peaksToRanges = void 0;
 const ml_spectra_processing_1 = require("ml-spectra-processing");
 const jAnalyzer_1 = __importDefault(require("./util/jAnalyzer"));
 const joinRanges_1 = require("./util/joinRanges");
@@ -246,6 +246,7 @@ function detectSignals(data, peakList, options = {}) {
     }
     return signals;
 }
+exports.detectSignals = detectSignals;
 /**
  * Return the area of a Lorentzian function
  * @param {object} peak - object with peak information

package/lib/peaks/peaksToRanges.js.map

@@ -1 +1 @@
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package/lib/peaks/solventSuppression.d.ts

@@ -0,0 +1,3 @@
+import { NMRSignal1D } from '../signals/NMRSignal1D';
+import { NMRPeak1D } from './NMRPeak1D';
+export declare function solventSuppression<T extends NMRPeak1D>(peakList: T[], solvent: NMRSignal1D[], options?: any): T[];

package/lib/peaks/solventSuppression.js

@@ -0,0 +1,155 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.solventSuppression = void 0;
+const linear_sum_assignment_1 = require("linear-sum-assignment");
+const ml_matrix_1 = require("ml-matrix");
+const ml_peak_shape_generator_1 = require("ml-peak-shape-generator");
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const addDummySignals_1 = require("../signals/addDummySignals");
+const signalsToSpinSystem_1 = require("../signals/simulation/signalsToSpinSystem");
+const simulateXYPeaks_1 = require("../signals/simulation/simulateXYPeaks");
+const splitSpinSystem_1 = require("../signals/simulation/splitSpinSystem");
+function solventSuppression(peakList, solvent, options = {}) {
+    const peaks = [...peakList].sort((a, b) => a.x - b.x);
+    const xValues = peaks.map((peak) => peak.x);
+    const { markSolventPeaks = false, solventZoneExtension = 1.2 } = options;
+    for (const solventSignal of solvent) {
+        let solventXYPeaks = solventSignal.peaks
+            ? solventSignal.peaks
+            : getSolventPeaks(solventSignal);
+        solventXYPeaks.sort((a, b) => a.x - b.x);
+        let upIndex = (0, ml_spectra_processing_1.xFindClosestIndex)(xValues, solventXYPeaks[solventXYPeaks.length - 1].x + solventZoneExtension);
+        let lowIndex = (0, ml_spectra_processing_1.xFindClosestIndex)(xValues, solventXYPeaks[0].x - solventZoneExtension);
+        if (upIndex === lowIndex)
+            continue;
+        const nearPeaks = peaks.slice(lowIndex, upIndex + 1);
+        const amplitudeResiduals = [];
+        const deltaResiduals = [];
+        const positionResiduals = [];
+        for (let peak of nearPeaks) {
+            const { peaks: shiftedSolventPeaks, delta: currentDelta } = getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks);
+            const closestPeaks = getClosestPeaks(shiftedSolventPeaks, nearPeaks);
+            let deltaResidual = 0;
+            let amplitudeResidual = 0;
+            let positionResidual = 0;
+            for (let i = 0; i < closestPeaks.length; i++) {
+                amplitudeResidual += Math.abs(shiftedSolventPeaks[i].y - closestPeaks[i].y);
+                deltaResidual += Math.abs(shiftedSolventPeaks[i].x - closestPeaks[i].x);
+            }
+            if (closestPeaks.length === 0) {
+                deltaResidual = Number.MAX_SAFE_INTEGER;
+                amplitudeResidual = Number.MAX_SAFE_INTEGER;
+                positionResidual = Number.MAX_SAFE_INTEGER;
+            }
+            else {
+                positionResidual = (0, ml_peak_shape_generator_1.gaussianFct)(Math.abs(solventSignal.delta - currentDelta), 0.5);
+            }
+            amplitudeResiduals.push(amplitudeResidual);
+            deltaResiduals.push(deltaResidual);
+            positionResiduals.push(positionResidual);
+        }
+        const maxAmplitude = (0, ml_spectra_processing_1.xMaxValue)(amplitudeResiduals);
+        const maxDelta = (0, ml_spectra_processing_1.xMaxValue)(deltaResiduals);
+        const maxPosition = (0, ml_spectra_processing_1.xMaxValue)(positionResiduals);
+        let minIndex = -1;
+        let minScore = Number.MAX_SAFE_INTEGER;
+        let score = [];
+        for (let i = 0; i < deltaResiduals.length; i++) {
+            const value = (amplitudeResiduals[i] / maxAmplitude +
+                deltaResiduals[i] / maxDelta +
+                1 -
+                positionResiduals[i] / maxPosition) /
+                3;
+            score.push(value);
+            if (minScore > value) {
+                minIndex = i;
+                minScore = value;
+            }
+        }
+        if (minScore < 0) {
+            new Error('There is not a correct match with the pattern');
+            return peaks;
+        }
+        const { peaks: shiftedSolventPeaks } = getShiftedSolventPeaks(nearPeaks[minIndex], solventSignal, solventXYPeaks);
+        const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+        const { rowAssignments, gain } = (0, linear_sum_assignment_1.linearSumAssignment)(diff, {
+            maximaze: false,
+        });
+        if (gain < 0) {
+            new Error('The gain is below to zero');
+            return peaks;
+        }
+        if (markSolventPeaks) {
+            for (let index of rowAssignments) {
+                peaks[index + lowIndex].kind = 'solvent';
+            }
+        }
+        else {
+            rowAssignments.sort((a, b) => b - a);
+            for (let index of rowAssignments) {
+                peaks.splice(index + lowIndex, 1);
+            }
+        }
+    }
+    return peaks;
+}
+exports.solventSuppression = solventSuppression;
+function getSolventPeaks(signal, options = {}) {
+    let signals = (0, addDummySignals_1.addDummySignals)([signal]);
+    let spinSystem = (0, signalsToSpinSystem_1.signalsToSpinSystem)(signals);
+    const { frequency = 400, maxClusterSize = 8 } = options;
+    spinSystem.clusters = (0, splitSpinSystem_1.splitSpinSystem)(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = (0, simulateXYPeaks_1.simulateXYPeaks)(spinSystem);
+    return peaks.filter((peak) => peak.x < 1000);
+}
+function getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks) {
+    const shiftedSolventPeaks = JSON.parse(JSON.stringify(solventXYPeaks));
+    // shift x values of solventPeaks to center it to the current peak.
+    let deltaPPM = peak.x - solventSignal.delta;
+    if (solventXYPeaks.length > 1 && solventXYPeaks.length % 2 === 0) {
+        deltaPPM += solventXYPeaks[0].x;
+    }
+    const maxIntensity = shiftedSolventPeaks.reduce((max, current) => (current.y > max ? current.y : max), shiftedSolventPeaks[0].y);
+    let currentDelta = 0;
+    for (let shiftedSolventPeak of shiftedSolventPeaks) {
+        shiftedSolventPeak.x += deltaPPM;
+        shiftedSolventPeak.y /= maxIntensity;
+        currentDelta += shiftedSolventPeak.x;
+    }
+    return {
+        peaks: shiftedSolventPeaks,
+        delta: currentDelta / shiftedSolventPeaks.length,
+    };
+}
+function getClosestPeaks(shiftedSolventPeaks, nearPeaks) {
+    const diff = getDiffMatrix(shiftedSolventPeaks, nearPeaks);
+    const { rowAssignments, gain } = (0, linear_sum_assignment_1.linearSumAssignment)(diff, {
+        maximaze: false,
+    });
+    if (gain === -1)
+        return [];
+    const assignmentPeaks = [];
+    let maxValue = Number.MIN_SAFE_INTEGER;
+    for (let index of rowAssignments) {
+        if (maxValue < nearPeaks[index].y)
+            maxValue = nearPeaks[index].y;
+        assignmentPeaks.push({ ...nearPeaks[index] });
+    }
+    assignmentPeaks.forEach((peak, i, arr) => (arr[i].y /= maxValue));
+    return assignmentPeaks;
+}
+function getDiffMatrix(rows, columns) {
+    const nbColumns = columns.length;
+    const nbRows = rows.length;
+    const diff = new ml_matrix_1.Matrix(nbRows, nbColumns);
+    for (let r = 0; r < nbRows; r++) {
+        for (let c = 0; c < nbColumns; c++) {
+            diff.set(r, c, Math.abs(rows[r].x - columns[c].x));
+        }
+    }
+    return diff;
+}
+//# sourceMappingURL=solventSuppression.js.map

package/lib/peaks/solventSuppression.js.map

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package/lib/peaks/util/jAnalyzer.d.ts

@@ -10,7 +10,7 @@ interface IntergralData {
     from: number;
     to: number;
 }
-export declare type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape' | 'fwhm'> & {
+export declare type Peak1DIntern = Omit<NMRPeak1D, 'y' | 'shape'> & {
     intensity: number;
 };
 export interface SignalIntern {

package/lib/peaks/util/jAnalyzer.js

@@ -10,11 +10,12 @@ let maxErrorIter1 = 2.5; // Hz
 let maxErrorIter2 = 1; // Hz
 let jAxisKeys = { jAxis: 'x', intensity: 'intensity' };
 function checkSignalForCompilePattern(signal) {
-    if (!signal.symRank) {
+    if (!('symRank' in signal)) {
         throw new Error('Internal error, symRank was not calculated');
     }
-    if (!signal.mask)
+    if (!('mask' in signal)) {
         throw new Error('Internal Error, mask was not added');
+    }
 }
 exports.default = {
     /**

package/lib/peaks/util/jAnalyzer.js.map

@@ -1 +1 @@
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package/lib/prediction/predictAllSpectra.d.ts

@@ -1,5 +1,5 @@
+import { FromTo, PointXY } from 'cheminfo-types';
 import type { Molecule } from 'openchemlib';
-import { OptionsSignalsToXY } from '../signals/signalsToXY';
 import { PredictAllOptions } from './predictAll';
 /**
  * This function will generate an object compatible with NMR-ium
@@ -7,12 +7,30 @@ import { PredictAllOptions } from './predictAll';
  * @param molecule
  * @param options
  */
-export declare function predictAllSpectra(molecule: Molecule, options?: {
+interface OneDOptions {
+    proton: FromTo;
+    carbon: FromTo;
+    nbPoints: number;
+    lineWidth: number;
+}
+interface TwoDOptions {
+    from: PointXY;
+    to: PointXY;
+    nbPoints: PointXY;
+}
+interface SimulationOptions {
+    frequency: number;
+    oneD?: Partial<OneDOptions>;
+    twoD?: Partial<TwoDOptions>;
+}
+interface PredictAllSpectraOptions {
     prediction?: PredictAllOptions;
-    simulation?: OptionsSignalsToXY;
-}): Promise<{
+    simulation?: SimulationOptions;
+}
+export declare function predictAllSpectra(molecule: Molecule, options?: PredictAllSpectraOptions): Promise<{
     spectra: any[];
     molecules: {
         molfile: any;
     }[];
 }>;
+export {};